Draft Genome Sequences of Novel Pseudomonas,
Flavobacterium, and Sediminibacterium Species Strains from a
Freshwater Ecosystem
Federica Pinto,aAdrian Tett,aFederica Armanini,aFrancesco Asnicar,aAdriano Boscaini,bEdoardo Pasolli,aMoreno Zolfo,a Claudio Donati,bNico Salmaso,b Nicola Segataa
aCentre for Integrative Biology, University of Trento, Trento, Italy bEdmund Mach Foundation, San Michele all’Adige, Italy
ABSTRACT Freshwater ecosystems represent 0.01% of the water on Earth, but they support 6% of global biodiversity that is still mostly uncharacterized. Here, we de-scribe the genome sequences of three strains belonging to novel species in the
Pseudomonas, Flavobacterium, and Sediminibacterium genera recovered from a water
sample of Lake Garda, Italy.
T
he uncharacterized microbial genetic diversity in natural environments is immense.Although high-throughput sequencing methods (1) and metagenomics (2) are recovering part of this diversity, ecosystems, such as freshwater habitats, which are estimated to support 6% of global biodiversity, remain poorly characterized (3). It is thus important to continue uncovering and analyzing microbial sequences from these environments.
In this project, we recovered and described three new microbial genomes of organisms inhabiting a pre-Alpine freshwater lake (Lake Garda, Italy). We specifically focused on potential symbionts of cyanobacterial organisms, and the genomic DNA was obtained from a nonaxenic culture of Tychonema bourrellyi (4). Paired-end libraries (Illumina) were prepared and run on the Illumina HiSeq 2500 platform (100-nucleo-tide [nt]-long paired-end reads). Raw reads were assembled using metaSPAdes version 3.10.1 (5) with default parameters, which generated 7,029 contigs larger than 1,000 bp with a total size of 74 Mbp. From this metagenomic assembly, three genomes belong-ing to the Pseudomonas, Flavobacterium, and Sediminibacterium genera were binned using the manually supervised anvi’o protocol based on the abundance and tetranucle-otide frequency distributions (6) and quality controlled by CheckM (7) (100%, 99%, and 99% predicted completeness, respectively, with an indication of contamination only for
Pseudomonas at 0.27% and no strain heterogeneity).
The Pseudomonas sp. strain FEMGT703P genome has 4.41 Mb assembled into 14
contigs, with an N50of 398,350 bp and a GC content of 59.93%. The assembly of the
Flavobacterium sp. strain FEMGT703F genome resulted in 2.98 Mb, with an N50 of
372,530 bp and a GC content of 38.68%. The Sediminibacterium sp. strain FEMGT703S
genome has 3.22 Mb, with an N50of 530,195 bases and a GC content of 35.78%. The
genomes were annotated using Prokka version 1.11 (8), which identified 4,064, 2,649, and 2,877 coding sequences for the Pseudomonas, Flavobacterium, and
Sediminibacte-rium genomes, respectively. High-resolution phylogenetic profiling using PhyloPhlAn
(9) and sequence similarity analysis using pyani (version 0.2.6; option “-m ANIb”) both confirmed that the three genomes belong to new species when using a sequence identity cutoff of 95%.
The discovery of these new three microbial genomes in a nonaxenic T. bourrellyi culture might confirm the establishment of an ecological association between
cyano-Received 4 January 2018 Accepted 5 January
2018 Published 1 February 2018
Citation Pinto F, Tett A, Armanini F, Asnicar F,
Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N. 2018. Draft genome sequences of novel Pseudomonas, Flavobacterium, and
Sediminibacterium species strains from a
freshwater ecosystem. Genome Announc 6:
e00009-18.https://doi.org/10.1128/genomeA
.00009-18.
Copyright © 2018 Pinto et al. This is an
open-access article distributed under the terms of theCreative Commons Attribution 4.0 International license.
Address correspondence to Nico Salmaso, nico.salmaso@fmach.it, or Nicola Segata, nicola.segata@unitn.it.
PROKARYOTES
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bacteria and heterotrophic microbes (10, 11). However, more investigations are still needed to further characterize the microbial community diversity and interactions in freshwater systems.
Accession number(s). The sequences for this genome project have been
depos-ited in GenBank under the accession no. PGCM00000000 (Pseudomonas sp.
FEMGT703P), PGCN00000000 (Flavobacterium sp. FEMGT703F), and PGCO00000000
(Sediminibacterium sp. FEMGT703S). The versions described in this paper are the first versions, PGCM01000000, PGCN01000000, and PGCO01000000, respectively.
ACKNOWLEDGMENTS
This work was financially supported by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 704603 to Federica Pinto and Marie Skłodowska-Curie grant agreement no. 707345 to Edoardo Pasolli and by the European Research Council (ERC-STG project MetaPG) to Nicola Segata.
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8. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioin-formatics 30:2068 –2069.https://doi.org/10.1093/bioinformatics/btu153. 9. Segata N, Börnigen D, Morgan XC, Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304.https://doi.org/10.1038/ncomms3304. 10. Alvarenga DO, Fiore MF, Varani AM. 2017. A metagenomic approach to
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Pinto et al.
Volume 6 Issue 5 e00009-18 genomea.asm.org 2
on September 13, 2018 by guest
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Correction for Pinto et al., “Draft Genome Sequences of Novel
Pseudomonas, Flavobacterium, and Sediminibacterium Strains
from a Freshwater Ecosystem”
Federica Pinto,aAdrian Tett,aFederica Armanini,aFrancesco Asnicar,aAdriano Boscaini,bEdoardo Pasolli,aMoreno Zolfo,a Claudio Donati,bNico Salmaso,b Nicola Segataa
aCentre for Integrative Biology, University of Trento, Trento, Italy bEdmund Mach Foundation, San Michele all’Adige, Italy
Volume 6, no. 5, e00009-18, 2018, https://doi.org/10.1128/genomeA.00009-18.
Page 1: The article title should read as given above.
Published 8 March 2018
Citation Pinto F, Tett A, Armanini F, Asnicar F,
Boscaini A, Pasolli E, Zolfo M, Donati C, Salmaso N, Segata N. 2018. Correction for Pinto et al., “Draft genome sequences of novel
Pseudomonas, Flavobacterium, and Sediminibacterium strains from a freshwater
ecosystem.” Genome Announc 6:e00169-18.
https://doi.org/10.1128/genomeA.00169-18.
Copyright © 2018 Pinto et al. This is an
open-access article distributed under the terms of theCreative Commons Attribution 4.0 International license.
AUTHOR CORRECTION
